YPMR - BACSU - GREMLIN Contacts

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YPMR - Uncharacterized protein YpmR

UniProt:	P40766	Sequences: MKLRIFSIMASLILLLTACTSIRTSSEGKQKAHETKTKEHIVIAAVGDSLTEGVGDPDGKGYVGKVADSIRSDKQVKTVDVKNYAVKGNRSDDLLEKLKDKKVQKGIKDADYVFFTIGGNDLMKILRQNFLQLTVEPFQEAEKPYEKRFEKIISEIRELNDHAELIYVSMYNPFTFTLSELNEINGVVTDWNHIAEKELKKDKHAKIVHIEDLFNQKSDSSRISEEDDFHPNGTGYSLIAKRVYQAIKKEGLPKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	255 (205)
Sequences:	4492 (3608)
Seq/√Len:	252.0

ECOLI - TESA
BACSU - YPMR LIPC YQEF RHGT1 RHGT2
SULSO - Q97UG8

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
169_S	207_I	4.607	1.00
146_E	197_K	3.553	1.00
150_E	201_K	3.215	1.00
43_I	114_F	3.211	1.00
94_L	117_I	2.967	1.00
168_V	243_V	2.611	1.00
209_H	212_D	2.610	1.00
169_S	209_H	2.536	1.00
154_S	203_K	2.445	1.00
150_E	203_K	2.315	1.00
164_E	206_K	2.234	1.00
52_E	87_K	2.221	1.00
196_E	200_K	2.127	1.00
242_R	245_Q	2.126	1.00
51_T	85_A	2.125	1.00
149_F	195_A	2.073	1.00
237_S	241_K	2.067	1.00
45_A	114_F	2.050	1.00
91_S	148_R	2.048	1.00
150_E	154_S	1.993	1.00
42_V	111_D	1.989	1.00
155_E	159_L	1.960	1.00
150_E	198_E	1.922	1.00
45_A	63_V	1.875	1.00
69_S	244_Y	1.867	1.00
41_I	111_D	1.862	1.00
45_A	51_T	1.859	1.00
167_Y	199_L	1.848	1.00
65_K	237_S	1.846	1.00
89_N	97_K	1.815	1.00
160_N	163_A	1.808	1.00
113_V	163_A	1.784	1.00
188_V	192_N	1.750	1.00
50_L	119_G	1.743	1.00
42_V	80_D	1.741	1.00
113_V	156_I	1.735	1.00
153_I	167_Y	1.721	1.00
54_V	87_K	1.719	1.00
99_K	155_E	1.694	1.00
89_N	93_D	1.652	1.00
95_L	151_K	1.643	1.00
91_S	149_F	1.604	1.00
146_E	194_I	1.558	1.00
153_I	205_A	1.554	1.00
166_I	208_V	1.554	1.00
189_T	211_E	1.533	1.00
210_I	239_I	1.512	1.00
196_E	207_I	1.497	1.00
149_F	167_Y	1.495	1.00
146_E	150_E	1.465	1.00
66_V	244_Y	1.449	1.00
95_L	148_R	1.445	1.00
236_Y	239_I	1.429	1.00
42_V	82_K	1.428	1.00
91_S	152_I	1.419	1.00
208_V	246_A	1.389	1.00
155_E	158_E	1.375	1.00
166_I	206_K	1.370	1.00
103_V	106_G	1.358	1.00
169_S	196_E	1.348	1.00
53_G	236_Y	1.340	1.00
197_K	201_K	1.337	1.00
112_Y	166_I	1.303	1.00
192_N	195_A	1.300	1.00
66_V	243_V	1.288	1.00
213_L	242_R	1.267	1.00
51_T	116_T	1.261	1.00
231_P	239_I	1.241	1.00
65_K	69_S	1.226	1.00
146_E	198_E	1.224	1.00
95_L	155_E	1.224	1.00
44_A	110_A	1.200	1.00
198_E	203_K	1.197	1.00
86_V	89_N	1.192	1.00
165_L	205_A	1.192	1.00
94_L	152_I	1.183	1.00
193_H	196_E	1.175	1.00
116_T	119_G	1.158	1.00
34_E	37_T	1.147	1.00
69_S	241_K	1.146	1.00
43_I	112_Y	1.136	1.00
123_M	229_F	1.111	1.00
151_K	154_S	1.099	1.00
45_A	66_V	1.095	1.00
42_V	109_D	1.083	1.00
145_Y	149_F	1.078	1.00
185_N	189_T	1.077	1.00
61_G	64_G	1.077	1.00
234_T	237_S	1.071	1.00
49_S	230_H	1.062	1.00
194_I	197_K	1.059	1.00
63_V	81_V	1.057	1.00
91_S	95_L	1.055	1.00
240_A	244_Y	1.053	1.00
84_Y	105_K	1.049	1.00
206_K	246_A	1.047	1.00
102_K	105_K	1.045	1.00
141_A	144_P	1.044	1.00
121_D	148_R	1.044	1.00
46_V	84_Y	1.013	1.00
50_L	171_Y	1.011	1.00
107_I	160_N	1.006	1.00
67_A	71_R	0.990	1.00
116_T	168_V	0.983	1.00
66_V	69_S	0.977	1.00
61_G	83_N	0.977	1.00
149_F	198_E	0.969	1.00
193_H	197_K	0.956	1.00
145_Y	191_W	0.952	1.00
238_L	241_K	0.946	1.00
50_L	236_Y	0.946	1.00
137_P	140_E	0.943	1.00
50_L	231_P	0.935	1.00
192_N	211_E	0.927	1.00
57_P	233_G	0.923	1.00
153_I	157_R	0.918	1.00
28_G	31_K	0.915	1.00
145_Y	195_A	0.913	1.00
149_F	152_I	0.907	1.00
175_T	183_E	0.907	1.00
54_V	236_Y	0.903	1.00
169_S	210_I	0.899	1.00
93_D	96_E	0.890	1.00
30_Q	33_H	0.888	1.00
199_L	207_I	0.887	1.00
44_A	84_Y	0.878	1.00
84_Y	106_G	0.871	1.00
64_G	68_D	0.861	0.99
119_G	229_F	0.859	0.99
90_R	93_D	0.854	0.99
178_L	181_L	0.853	0.99
65_K	68_D	0.850	0.99
176_F	180_E	0.847	0.99
90_R	124_K	0.840	0.99
91_S	117_I	0.840	0.99
56_D	61_G	0.839	0.99
153_I	198_E	0.830	0.99
46_V	94_L	0.827	0.99
65_K	240_A	0.823	0.99
156_I	163_A	0.822	0.99
101_K	105_K	0.821	0.99
151_K	155_E	0.821	0.99
233_G	237_S	0.820	0.99
62_Y	243_V	0.820	0.99
56_D	59_G	0.820	0.99
231_P	236_Y	0.817	0.99
144_P	148_R	0.813	0.99
136_E	139_Q	0.812	0.99
30_Q	34_E	0.810	0.99
157_R	165_L	0.809	0.99
195_A	207_I	0.808	0.99
65_K	236_Y	0.804	0.99
167_Y	195_A	0.803	0.99
149_F	153_I	0.802	0.99
98_L	156_I	0.800	0.99
85_A	97_K	0.800	0.99
28_G	32_A	0.795	0.99
101_K	106_G	0.794	0.99
177_T	180_E	0.793	0.99
214_F	235_G	0.791	0.99
198_E	201_K	0.789	0.99
41_I	79_V	0.789	0.99
46_V	98_L	0.784	0.99
145_Y	194_I	0.782	0.99
121_D	235_G	0.780	0.99
143_K	194_I	0.775	0.99
224_S	227_D	0.775	0.99
115_F	156_I	0.775	0.99
139_Q	190_D	0.763	0.99
117_I	149_F	0.761	0.99
161_D	164_E	0.760	0.99
62_Y	114_F	0.757	0.99
31_K	36_K	0.754	0.99
28_G	33_H	0.754	0.99
170_M	191_W	0.750	0.99
172_N	185_N	0.747	0.99
92_D	148_R	0.743	0.98
140_E	144_P	0.743	0.98
101_K	104_Q	0.741	0.98
51_T	63_V	0.741	0.98
95_L	152_I	0.740	0.98
64_G	67_A	0.729	0.98
83_N	86_V	0.727	0.98
196_E	209_H	0.727	0.98
43_I	81_V	0.725	0.98
172_N	189_T	0.719	0.98
102_K	106_G	0.718	0.98
63_V	70_I	0.712	0.98
146_E	201_K	0.711	0.98
142_E	146_E	0.706	0.98
142_E	194_I	0.704	0.98
57_P	60_K	0.704	0.98
194_I	198_E	0.696	0.98
29_K	35_T	0.695	0.98
32_A	37_T	0.695	0.98
143_K	147_K	0.695	0.98
51_T	171_Y	0.693	0.98
107_I	110_A	0.689	0.97
161_D	165_L	0.689	0.97
152_I	155_E	0.689	0.97
234_T	238_L	0.688	0.97
28_G	34_E	0.687	0.97
147_K	151_K	0.687	0.97
63_V	66_V	0.683	0.97
77_K	80_D	0.681	0.97
67_A	70_I	0.681	0.97
179_S	182_N	0.676	0.97
32_A	36_K	0.676	0.97
238_L	242_R	0.661	0.97
214_F	238_L	0.660	0.97
69_S	240_A	0.658	0.97
107_I	159_L	0.657	0.97
104_Q	159_L	0.655	0.97
104_Q	108_K	0.655	0.97
212_D	242_R	0.654	0.97
40_H	111_D	0.652	0.97
235_G	239_I	0.651	0.96
91_S	98_L	0.642	0.96
167_Y	205_A	0.641	0.96
143_K	146_E	0.640	0.96
48_D	119_G	0.640	0.96
85_A	236_Y	0.640	0.96
63_V	67_A	0.640	0.96
113_V	165_L	0.637	0.96
41_I	112_Y	0.635	0.96
185_N	188_V	0.634	0.96
85_A	235_G	0.631	0.96
159_L	163_A	0.630	0.96
95_L	99_K	0.626	0.96
168_V	210_I	0.622	0.95
120_N	230_H	0.622	0.95
142_E	190_D	0.620	0.95
186_G	190_D	0.618	0.95
191_W	195_A	0.617	0.95
43_I	62_Y	0.615	0.95
199_L	204_H	0.614	0.95
32_A	35_T	0.613	0.95
62_Y	66_V	0.612	0.95
33_H	36_K	0.611	0.95
70_I	73_D	0.609	0.95
94_L	97_K	0.608	0.95
98_L	152_I	0.608	0.95
30_Q	35_T	0.606	0.95
173_P	229_F	0.605	0.95
103_V	155_E	0.604	0.95
55_G	229_F	0.602	0.95
110_A	160_N	0.601	0.95
137_P	141_A	0.601	0.95
157_R	205_A	0.598	0.94
52_E	119_G	0.595	0.94
45_A	81_V	0.592	0.94
153_I	203_K	0.591	0.94
157_R	203_K	0.591	0.94
208_V	242_R	0.591	0.94
92_D	96_E	0.590	0.94
214_F	242_R	0.590	0.94
29_K	32_A	0.589	0.94
49_S	120_N	0.587	0.94
116_T	171_Y	0.587	0.94
213_L	238_L	0.585	0.94
29_K	37_T	0.584	0.94
30_Q	37_T	0.578	0.93
56_D	233_G	0.578	0.93
86_V	93_D	0.575	0.93
61_G	236_Y	0.575	0.93
110_A	163_A	0.571	0.93
89_N	119_G	0.570	0.93
232_N	235_G	0.570	0.93
242_R	246_A	0.570	0.93
208_V	243_V	0.568	0.93
186_G	200_K	0.568	0.93
62_Y	67_A	0.567	0.93
51_T	62_Y	0.562	0.92
117_I	120_N	0.561	0.92
147_K	150_E	0.561	0.92
66_V	240_A	0.561	0.92
56_D	86_V	0.558	0.92
170_M	192_N	0.555	0.92
105_K	108_K	0.553	0.92
89_N	117_I	0.547	0.91
199_L	205_A	0.547	0.91
177_T	182_N	0.543	0.91
45_A	62_Y	0.543	0.91
136_E	140_E	0.543	0.91
39_E	42_V	0.542	0.91
94_L	115_F	0.537	0.91
166_I	247_I	0.535	0.90
115_F	152_I	0.534	0.90
175_T	181_L	0.524	0.89
225_E	228_D	0.523	0.89
85_A	232_N	0.521	0.89
157_R	204_H	0.520	0.89
99_K	207_I	0.518	0.89
148_R	151_K	0.516	0.89
172_N	188_V	0.512	0.88
41_I	72_S	0.512	0.88
91_S	145_Y	0.512	0.88
193_H	198_E	0.512	0.88
116_T	169_S	0.510	0.88
35_T	38_K	0.509	0.88
186_G	189_T	0.506	0.88
138_F	141_A	0.505	0.88
69_S	237_S	0.504	0.88
212_D	215_N	0.502	0.87
69_S	72_S	0.502	0.87
113_V	160_N	0.501	0.87
44_A	82_K	0.501	0.87
190_D	193_H	0.500	0.87

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4q9aA	2	0.8118	100	0.389	Contact Map
1escA	1	0.8275	100	0.396	Contact Map
4hyqA	1	0.7804	100	0.41	Contact Map
4jggA	1	0.7059	100	0.421	Contact Map
3bzwA	4	0.8353	100	0.423	Contact Map
1vjgA	2	0.7725	100	0.434	Contact Map
3rjtA	2	0.7961	100	0.437	Contact Map
4rw0A	1	0.7216	100	0.44	Contact Map
4jhlA	5	0.8157	100	0.44	Contact Map
3dc7A	3	0.7843	100	0.441	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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